Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF MECA
 
Authors :  F. Wang, Z. Mei, Y. Qi, C. Yan, J. Wang, Y. Shi
Date :  14 Sep 09  (Deposition) - 29 Sep 09  (Release) - 29 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Meca; Adaptor Protein; Degradation Tag, Competence, Sporulation, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Wang, Z. Mei, Y. Qi, C. Yan, S. Xiang, Z. Zhou, Q. Hu, J. Wang, Y. Shi
Crystal Structure Of The Meca Degradation Tag
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADAPTER PROTEIN MECA 1
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN, UNP RESIDUES 121-218
    Gene: MECA
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 35)

Asymmetric Unit (1, 35)
No.NameCountTypeFull Name
1IOD35Ligand/IonIODIDE ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1IOD8Ligand/IonIODIDE ION
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1IOD8Ligand/IonIODIDE ION
Biological Unit 3 (1, 8)
No.NameCountTypeFull Name
1IOD8Ligand/IonIODIDE ION
Biological Unit 4 (1, 10)
No.NameCountTypeFull Name
1IOD10Ligand/IonIODIDE ION

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:55BINDING SITE FOR RESIDUE IOD A 101
02AC2SOFTWAREARG A:13 , ARG A:41BINDING SITE FOR RESIDUE IOD A 102
03AC3SOFTWAREARG A:76BINDING SITE FOR RESIDUE IOD A 103
04AC4SOFTWARETYR A:80 , LYS C:25 , HOH C:119BINDING SITE FOR RESIDUE IOD A 104
05AC5SOFTWAREIOD A:107BINDING SITE FOR RESIDUE IOD A 106
06AC6SOFTWAREIOD A:106BINDING SITE FOR RESIDUE IOD A 107
07AC7SOFTWAREARG B:76BINDING SITE FOR RESIDUE IOD B 100
08AC8SOFTWAREARG B:13 , ARG B:41BINDING SITE FOR RESIDUE IOD B 101
09AC9SOFTWARELYS B:25 , SER B:99 , GLU C:39BINDING SITE FOR RESIDUE IOD B 102
10BC1SOFTWAREGLU B:87BINDING SITE FOR RESIDUE IOD B 104
11BC2SOFTWAREGLU B:39BINDING SITE FOR RESIDUE IOD B 105
12BC3SOFTWAREGLU B:79BINDING SITE FOR RESIDUE IOD B 106
13BC4SOFTWAREGLU B:79BINDING SITE FOR RESIDUE IOD B 107
14BC5SOFTWAREARG C:13 , ARG C:41BINDING SITE FOR RESIDUE IOD C 100
15BC6SOFTWAREASN C:40BINDING SITE FOR RESIDUE IOD C 102
16BC7SOFTWAREILE B:85BINDING SITE FOR RESIDUE IOD C 103
17BC8SOFTWAREASN C:29 , THR C:33 , GLU C:91BINDING SITE FOR RESIDUE IOD C 104
18BC9SOFTWARESER C:99BINDING SITE FOR RESIDUE IOD C 105
19CC1SOFTWAREIOD C:107BINDING SITE FOR RESIDUE IOD C 106
20CC2SOFTWAREHIS C:88 , IOD C:106BINDING SITE FOR RESIDUE IOD C 107
21CC3SOFTWAREGLY D:15 , ARG D:41BINDING SITE FOR RESIDUE IOD D 1
22CC4SOFTWAREILE D:74BINDING SITE FOR RESIDUE IOD D 100
23CC5SOFTWARELYS A:25 , SER A:99 , GLU D:39BINDING SITE FOR RESIDUE IOD D 101
24CC6SOFTWARETHR C:52 , ASP C:53BINDING SITE FOR RESIDUE IOD D 102
25CC7SOFTWAREARG C:76 , GLU D:79BINDING SITE FOR RESIDUE IOD D 103
26CC8SOFTWAREIOD D:108BINDING SITE FOR RESIDUE IOD D 104
27CC9SOFTWAREHIS D:75 , IOD D:106BINDING SITE FOR RESIDUE IOD D 105
28DC1SOFTWAREILE A:62 , SER D:73 , ARG D:76 , IOD D:105BINDING SITE FOR RESIDUE IOD D 106
29DC2SOFTWAREASP C:50 , MET C:51BINDING SITE FOR RESIDUE IOD D 107
30DC3SOFTWARESER D:86 , IOD D:104BINDING SITE FOR RESIDUE IOD D 108

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JTP)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly C:30 -Ser C:31

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JTP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JTP)

(-) Exons   (0, 0)

(no "Exon" information available for 3JTP)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:92
 aligned with MECA1_BACSU | P37958 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:92
                                   136       146       156       166       176       186       196       206       216  
          MECA1_BACSU   127 LQFVLRFGDFEDVISLSKLNVNGSKTTLYSFENRYYLYVDFCNMTDEEVENQLSILLEYATESSISIHRLEEYGKLIISEHALETIKKHFAS 218
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhh.....eeeeeee..eeeeeee......hhhhhhhhhhhhhhee...hhhhhhhhheeee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 3jtp A   8 LQFVLRFGDFEDVISLSKLNVNGSKTTLYSFENRYYLYVDFCDMTDEEVENQLSIMLEYANESSISIHRLEEYGKLIISEHALETIKKHFAS  99
                                    17        27        37        47        57        67        77        87        97  


Chain B from PDB  Type:PROTEIN  Length:93
 aligned with MECA1_BACSU | P37958 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:93
                                   135       145       155       165       175       185       195       205       215   
          MECA1_BACSU   126 KLQFVLRFGDFEDVISLSKLNVNGSKTTLYSFENRYYLYVDFCNMTDEEVENQLSILLEYATESSISIHRLEEYGKLIISEHALETIKKHFAS 218
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhh.....eeeeeee..eeeeeee....hhhhhhhhhhhhh...ee...hhhhhhhhheeee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 3jtp B   7 KLQFVLRFGDFEDVISLSKLNVNGSKTTLYSFENRYYLYVDFCDMTDEEVENQLSIMLEYANESSISIHRLEEYGKLIISEHALETIKKHFAS  99
                                    16        26        36        46        56        66        76        86        96   


Chain C from PDB  Type:PROTEIN  Length:93
 aligned with MECA1_BACSU | P37958 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:93
                                   135       145       155       165       175       185       195       205       215   
          MECA1_BACSU   126 KLQFVLRFGDFEDVISLSKLNVNGSKTTLYSFENRYYLYVDFCNMTDEEVENQLSILLEYATESSISIHRLEEYGKLIISEHALETIKKHFAS 218
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhh......eeeeeee..eeeeeee....hhhhhhhhhhhhh...ee...hhhhhhhhheeee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 3jtp C   7 KLQFVLRFGDFEDVISLSKLNVNGSKTTLYSFENRYYLYVDFCDMTDEEVENQLSIMLEYANESSISIHRLEEYGKLIISEHALETIKKHFAS  99
                                    16        26        36        46        56        66        76        86        96   


Chain D from PDB  Type:PROTEIN  Length:93
 aligned with MECA1_BACSU | P37958 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:93
                                   135       145       155       165       175       185       195       205       215   
          MECA1_BACSU   126 KLQFVLRFGDFEDVISLSKLNVNGSKTTLYSFENRYYLYVDFCNMTDEEVENQLSILLEYATESSISIHRLEEYGKLIISEHALETIKKHFAS 218
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) MecA-3jtpD01 D:7-95                                                                      ---- Pfam domains (1)
           Pfam domains (2) MecA-3jtpD02 D:7-95                                                                      ---- Pfam domains (2)
           Pfam domains (3) MecA-3jtpD03 D:7-95                                                                      ---- Pfam domains (3)
           Pfam domains (4) MecA-3jtpD04 D:7-95                                                                      ---- Pfam domains (4)
         Sec.struct. author ..eeeeee.hhhhhhhhhh......eeeeeee..eeeeeee......hhhhhhhhhhh...ee...hhhhhhhhheeee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 3jtp D   7 KLQFVLRFGDFEDVISLSKLNVNGSKTTLYSFENRYYLYVDFCDMTDEEVENQLSIMLEYANESSISIHRLEEYGKLIISEHALETIKKHFAS  99
                                    16        26        36        46        56        66        76        86        96
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3JTP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JTP)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: MecA] (5)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (MECA1_BACSU | P37958)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
biological process
    GO:0030420    establishment of competence for transformation    The process in which a naturally transformable bacterium acquires the ability to take up exogenous DNA. This term should be applied only to naturally transformable bacteria, and should not be used in the context of artificially induced bacterial transformation.
    GO:0045808    negative regulation of establishment of competence for transformation    Any process that stops, prevents, or reduces the frequency, rate or extent of establishment of competence for transformation.
    GO:0042174    negative regulation of sporulation resulting in formation of a cellular spore    Any process that stops, prevents, or reduces the frequency, rate or extent of sporulation.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    IOD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
    CC6  [ RasMol ]  +environment [ RasMol ]
    CC7  [ RasMol ]  +environment [ RasMol ]
    CC8  [ RasMol ]  +environment [ RasMol ]
    CC9  [ RasMol ]  +environment [ RasMol ]
    DC1  [ RasMol ]  +environment [ RasMol ]
    DC2  [ RasMol ]  +environment [ RasMol ]
    DC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly C:30 - Ser C:31   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3jtp
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MECA1_BACSU | P37958
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MECA1_BACSU | P37958
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MECA1_BACSU | P37958: 2y1r 3j3r 3j3s 3j3t 3j3u 3pxg 3pxi

(-) Related Entries Specified in the PDB File

3jtn 3jto